Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4708 to 4757 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2354 signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Divided 5516.67 5758.22 1.04379
2355 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 5262.6 5492.58 1.0437
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Subtracted 3591.95 3375.34 216.61
2356 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Divided 5515.12 5755.63 1.04361
2357 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Subtracted 3591.95 3375.34 216.61
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Divided 5514.85 5755.17 1.04358
2358 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 3591.95 3375.34 216.61
signal transducer and activator of transcription 4. [swissprot;acc:q14765] Divided 5514.83 5755.14 1.04358
2359 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Subtracted 3591.95 3375.34 216.61
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] Divided 5514.81 5755.1 1.04357
2360 40s ribosomal protein s11. [swissprot;acc:p04643] Subtracted 3618.46 3402.09 216.37
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Divided 3843.06 3682.72 1.04354
2361 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Subtracted 8186.02 7971.27 214.75
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Divided 4674.38 4877.31 1.04341
2362 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 3598.08 3384.59 213.49
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Divided 4673.96 4876.71 1.04338
2363 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 3678.56 3470.55 208.01
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Divided 6822.6 6539.8 1.04324
2364 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 3678.62 3470.64 207.98
glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Divided 6822.6 6539.8 1.04324
2365 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 5254.55 5480.56 1.04301
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Subtracted 6963.12 7170.02 206.9
2366 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 4674.38 4877.31 202.93
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Divided 5265.95 5492.28 1.04298
2367 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Subtracted 4673.96 4876.71 202.75
fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Divided 5265.95 5492.28 1.04298
2368 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 3637.47 3435.61 201.86
mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Divided 5265.95 5492.28 1.04298
2369 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 4668.29 4868.52 200.23
fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Divided 5265.95 5492.28 1.04298
2370 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 3559.49 3360.39 199.1
2371 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Divided 4668.29 4868.52 1.04289
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Subtracted 8542.13 8740.23 198.1
2372 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Divided 3677.53 3526.65 1.04278
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Subtracted 5333.6 5531.41 197.81
2373 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 5078.5 5275.76 197.26
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Divided 3677.53 3526.65 1.04278
2374 40s ribosomal protein s21. [swissprot;acc:p35265] Subtracted 5078.5 5275.76 197.26
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Divided 3669.57 3520.86 1.04224
2375 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Subtracted 5078.5 5275.76 197.26
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Divided 3650.02 3502.81 1.04203
2376 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 3976.48 3816.38 1.04195
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Subtracted 5078.5 5275.76 197.26
2377 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Divided 3977.7 3818.01 1.04183
2378 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Subtracted 5078.5 5275.76 197.26
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Divided 3977.76 3818.09 1.04182
2379 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 3979.06 3819.84 1.04168

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/